I have some far-off plan to acquire a capital ship. But it needs a lot of crew members. I considered hiring NPCs, but the overall cost for their salary per month is extraordinary.

Since custom NPCs don't need a salary it would be convenient to have them for crew instead. So my question is "Would it be possible to have Custom NPC inside a ship and count them as a part of the crew?".

At the moment Crew Requirementis nothing you have to worry about. When it was initially added, the plan was for invisible NPCs to be picked up from planets/stations - it would just be a number that changed on your ship, much like cargo capacity does as you load/unload stuff. These NPCs would then charge you X amount each month. If you didn't pay, they would leave and the ships wouldn't be able to function as well.

However, at the moment, its not implemented, and as far as I am aware not in the immediate horizon. It may be brought in later, but I suspect code issues with the game generating such large numbers of events etc will cause problems for the rest of the game (such as salaries for normal NPCs, which has been deactivated until the code is smoothed out to avoid issues).